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As Deoxys hurls out its powerful psychoboost which rapidly spans out as a blinding energy explosion, Red barely has time to react, and Bill cries in horror as the attack swiftly consumes the boy. Just as the force is about to rip Red into pieces, his full team of Pokémon throw themselves in front of him to take the hit, and use all their might to withstand the excruciating pain inflicted by the deadly blast. When the attack finally passes, Pika, Saur, Poli, Lax, Gyara and Aero all collapse onto the ground unconscious, and Red falls to his knees with disbelief as he watches the smoke and dust rise from the badly injured bodies of his fallen companions.

Meanwhile, at the Sevault Canyon of Seven Island, Lorelei is battling it out with Storc of the Beast Warrior Trio. Fighting amid the rocky shore along the southern coast, Storc's Starmie delivers a powerful hydropump, but Lorelei's Jynx easily counters it with a blizzard. Suddenly, Lorelei notices the evening sky being lit up by a blinding light in the direction of Five Island, and wonders if Red is doing alright. However, this momentary distraction has allowed Storc's Persian to ambush with a slash, which Lorelei narrowly evades, and the TR secret agent grins that they should perhaps concentrate on their battle there.

Irritated, Lorelei sends out Slowking to join in the fight, and states that Team Rocket will not be able to outsmart her at the Sevii Islands, the place where she grew up. She suggests them abandoning their pointless attacks on the islands right away and leave, and proceeds to have Jynx blast Starmie back with another blizzard, and command a slam from Slowking to pin Persian onto the rocks, fainting it on the spot.

Storc grins that Kanto's Elite Four members truly live up to their reputation, and feels grateful that she has made preparations and recuited backup forces for the potentially long battle. Lorelei wonders what she is talking about, and the evil woman snaps her fingers, instanting causing a vigorous tremble across the island. Storc reveals that she has already unlocked the Tanoby Key, and Lorelei gasps in disbelief that the ancient seal of the Tanoby Ruins has been broken.

Off the southern coast of the Sevault Canyon are seven separate floating isles each with a mysterious chamber built on them, namely the Monean, Liptoo, Weepth, Dilford, Scufib, Rixy and Viapois Chambers. For a long time, no one has discovered the secret to these empty ancient ruins, and very few know about the purpose of the Tanoby Key cave. However, the Beast Warrior Trio have somehow uncovered the mystery that lies within, and even lifted the seal on a unique species of Pokémon inhabiting the chambers.

As the tremble across the island gradually subsides, a dark cloud is seen looming across the sky from the direction of the Tanoby Ruins. It soon materializes itself as a swarm of Unowns, and Lorelei jumps with surprise as the symbol Pokémon dive down towards them, and quickly plague over Slowking and Jynx. The combined hidden power attack of the beings faint her two Pokémon in no time, and Lorelei finds it hard to believe not only because such an ancient seal is so easily broken, but that Team Rocket also manages to assert control over the Unowns and bring them out of the ruin chambers.

However, the Elite Four trainer is not ready to give up as yet. Calling out her Cloyster, she decides to take care of the Unowns altogether, and commands a spike cannon. The bivalve Pokémon shoots out a barrage of sharp missiles in every direction, and the Unowns soon fall like flies while Storc hops between the rocks to dodge the attack. Lorelei puts on a victorious grin and wonders Storc will surrender now, but the evil woman squints her eyes with mockery, and smirks that Lorelei has in fact lost the battle already.

One of the rock boulders right in front of Cloyster suddenly begins to glow with a red light, and Lorelei notices with a start that it is actually the core of Starmie. Totally taken by surprise by the star-shaped Pokémon's sudden close proximity, she frantically tells Cloyster to close up its shell and throws herself in front of it, but it is too late. Starmie unleashes a hyperbeam onto the vulnerable innards of its foe, and at the same time, strikes Lorelei with the attack as well. The young woman slowly collapses onto the ground next to her fainted Pokémon, and realizes that Starmie has used camouflage to hide itself.

Storc grins that she knew Cloyster is Lorelei's toughest Pokémon to take down, as aside from its powerful spike cannon which is capable of hitting more than one opponent at a time, its hard shell is technically impregnable to all attacks, and couldn't even be shattered with a bomb. That is why she has picked the rocky shore as their battle ground, and made use of Starmie's camouflage skill to sneak up on Cloyster while it is distracted by the Unowns.

Lorelei grunts that it is despicable to unseal the Unowns simply for that reason, but Storc laughs that being despicable is Team Rocket's style, and switches on her handfree speakerphone to contact Giovanni, who is currently at the Trainer Tower to the northern coast of Seven Island. Storc reports on her victory before inquiring about the status of the polishing of the stone plates, and the TR leader states that the process is already completed. He praises the Beast Warrior Trio for hard work and buying him adequate time for it, but Storc assures him that they were simply enjoying their job.

Giovanni then informs Storc about Jagura's progress on Five Island, and reveals that Deoxys, whom he refers to as Individual 2, has finally showed up. While the creature is still incapable of fully activating its normal form, its attack and defence states have been confirmed to exist. Storc feels elated that their prediction is correct, and remarks that all they have to do now is to use the two energy-charged stone plates at hand, and they will be able to unlock all of Deoxys's remaining forms. She offers to come over to the Trainer Tower to pick up the stones right away, and Giovanni praises her once again for her promptness.

Sprawled across the rocky boulders, Lorelei gradually slips into unconsciousness as the pain from her injuries overwhelm her, but her fallen Jynx comes around before Storc is about to leave, and manages to secretly unleash a cold swirl of air around the TR secret agent's left ankle before she takes off on her Starmie.

On One Island, Blue has successfully slipped out from the Pokemon Network Center, and is panting to catch her breath in one of the narrow alleys. However, a torch light is suddenly shone on her face, and she realizes that she has been spotted by one of the island residents hunting down Red, Green and herself. The man quickly calls for assistance from two other guys, and the three of them start chasing after Blue who speeds away as fast as she can.

Blue soon finds herself cornered at the harbour, and thinks hard to come up with a plan as her pursuers edge closer. But just as the men are about to jump out and grasp her, they quickly back off in horror, and Blue turns around to see that the Sea Gallop is sailing right into them. The sailor manages to pull his liner to a halt before it crashes, and Brinca quickly tosses a rope down to Blue. The girl grabs it without a second thought, but the three men throw themselves at her and hold her down before Brinca could pull her up.

Fortunately, Celio arrives at the scene just in time, and tackles down the men to free Blue from their restraints. The three men furiously demand to know what Celio is doing, and toss him aside before going after Blue again. Brinca then calls out her Feraligatr which is blessed with the ability torrent, and has it fend the men off with a powerful stream of water. Celio tosses Blue back the Pokéballs of her healed Pokémon which are secured on a belt, and the girl thanks him as Brinca pulls the rope up with her staff. Watching the Sea Gallop sail away again, the three men recover from Feraligatr's attack, and start taking out their rage on Celio.

A while later, Green has left Six Island and is flying towards Five Island on Charizard. Unable to find out where Prof. Oak is held captive at from the fainted Oca, the boy decides to head over to join Red, and tells Charizard to hurry. Just then, he sees the Sea Gallop below sailing for Five Island as well, and orders his fire dragon to land on the ship. However, something fast moving suddenly speeds off from Five Island, and knocks him off Charizard before continuing south. Green crashes onto a glass table on the deck of the Sea Gallop, and Brinca, Blue and the sailor who are on board hurriedly rush over to check on him.

Green grunts with frustration, and looks up into the sky to see the orange and aqua green creature shooting off in an entirely new form again, this time with the back of its head elongated, and an extremely streamlined body with only one tentacle on each side. Recalling the two forms they've seen before, one in Blue's Silph. Scope and the other being the form Ditto transforms into, he wonders just how many appearances this enemy is capable of adopting.

The Sea Gallop soon docks at the harbour of Five Island, and Bill frantically motions them over with a desperate look on his face. Green and Blue gasp in shock when they see Red's fallen team, and dash over to their companion. Kneeling on the ground, Red seems a little disoriented when he sees his friends, but is glad that Blue has come around from her coma. Green asks with a worried tone if Red has just faced the mysterious Pokémon, but Red simply puts on a weak grin and says his strength and skills weren't up for the challenge. Taking another look at his six battered Pokémon, the boy declares that he has officially lost…